Receptor Marker

Installation

This package should be installed directly from GitHub using the devtools package. The Bioconductor package muscle is a dependency that must be installed first - follow Bioconductor's instructions. Then, to install receptormarker:

install.packages("devtools")
devtools::install_github('nsh87/receptormarker')

Further Note

This package is currently only tested on Unix (Linux/Mac OS X) environments. Functionality in Windows might be limited due to the unavailability of Windows binaries for included analytical tools.

We will not be making receptormarker available through CRAN or Bioconductor. We include a number of dependencies and binary files used for analysis (such as HMMER and standalone BLAST) so that the user does not need to have these tools previously installed on his or her computer. This eases use of the package but also prevents it from conforming to CRAN's guidelines.

Development

Fork the repository, branch from dev, and submit your branch changes with a pull request to dev.

To get started, make sure you have the latest version of R and RStudio installed. It is strongly suggested - nay, required - that you have installed the following packages in order to develop:

install.packages(c("devtools", "roxygen2", "testthat", "knitr", "htmlwidgets"))
devtools::install_github('jimhester/lintr')  # Do not install from CRAN

You also need to install muscle from Bioconductor (see link in Installation).

Clone this repo and load receptormarker.Rproj to open the project in RStudio. Then load the code:

devtools::load_all()

Be sure to follow this [code tyle](http://r-pkgs.had.co.nz/r.html#style "Hadley Wickham's Modified Google R Style Guide") and document your functions. If you create any functions that are internal and not of interest to most users, be sure to document them with @keywords internal to exclude them from the package index. You should explicitly define functions to export to NAMESPACE with Roxygen2's @export tag. Build .Rd files from Roxygen2 comments with:

devtools::document()

It is strongly suggested that you automate testing of all functions written. Run all tests with:

devtools::test()

Before submitting a pull request you should build the documentation, run tests, and check that the package builds. This can be done with a single command:

devtools::check(cran=FALSE)

Note that we are not checking the package --as-cran since we have included HMMER and BLAST+ binaries and CRAN does not allow executable binaries in packages.

You can also load the package and then test functions after running:

devtools::install()
library(receptormarker)

Installing the package is not required to run many functions locally, but for any functions that use htmlwidgets this is a necessary step.